Search results for the GEO ID: GSE7788  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM188662 | GPL570 |
|
NLPHL_lymph_node_case1
|
lymph node affected by NLPHL
|
Gender: male, Age: 49, Tissue: lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage: IA, follow-up: 10 years; status at last follow-up: died of squamous cell carcinoma of the larynx
|
Nodular lymphocyte predominant Hodgkin's lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188662
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188662/suppl/GSM188662.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188663 | GPL570 |
|
THRBL_lymph_node_case1
|
lymph node affected by THRBL
|
Gender: female, Age: 50, Tissue: lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage: IVB, IPI prognostic score: low intermediate, follow-up: 3 years; status at last follow-up: death with disease
|
T cell/histiocyte rich B cell lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188663
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188663/suppl/GSM188663.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188664 | GPL570 |
|
NLPHL_lymph_node_case2
|
lymph node affected by NLPHL
|
Gender: female, Age: 71, Tissue: lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage: IIIB, follow-up: 5 years; status at last follow-up: alive with disease
|
Nodular lymphocyte predominant Hodgkin's lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188664
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188664/suppl/GSM188664.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188665 | GPL570 |
|
THRBL_lymph_node_case2
|
lymph node affected by THRBL
|
Gender: male, Age: 67, Tissue: lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage: IVB, IPI prognostic score: high intermediate, follow-up: 2 years; status at last follow-up: death with disease
|
T cell/histiocyte rich B cell lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188665
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188665/suppl/GSM188665.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188666 | GPL570 |
|
NLPHL_lymph_node_case3
|
lymph node affected by NLPHL
|
Gender: male, Age: 63, Tissue: lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage: I, follow-up: lost for follow-up
|
Nodular lymphocyte predominant Hodgkin's lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188666
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188666/suppl/GSM188666.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188667 | GPL570 |
|
NLPHL_lymph_node_case4
|
lymph node affected by NLPHL
|
Gender: male, Age: 43, Tissue: lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage: IA, follow-up: 6 years; status at last follow-up: alive without disease
|
Nodular lymphocyte predominant Hodgkin's lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188667
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188667/suppl/GSM188667.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188668 | GPL570 |
|
NLPHL_lymph_node_case5
|
lymph node affected by NLPHL
|
Gender: male, Age: 67, Tissue: lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage: IIA, follow-up: 8 years; status at last follow-up: died of squamous cell carcinoma of the lung
|
Nodular lymphocyte predominant Hodgkin's lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188668
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188668/suppl/GSM188668.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188669 | GPL570 |
|
NLPHL_lymph_node_case6
|
lymph node affected by NLPHL
|
Gender: female, Age: 22, Tissue: lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage: IIB, follow-up: 10 years; status at last follow-up: alive without disease
|
Nodular lymphocyte predominant Hodgkin's lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188669
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188669/suppl/GSM188669.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188670 | GPL570 |
|
NLPHL_lymph_node_case7
|
lymph node affected by NLPHL
|
Gender: male, Age: 42, Tissue: lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage: IIA, follow-up: 10 years; status at last follow-up: alive without disease
|
Nodular lymphocyte predominant Hodgkin's lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188670
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188670/suppl/GSM188670.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188671 | GPL570 |
|
NLPHL_lymph_node_case8
|
lymph node affected by NLPHL
|
Gender: male, Age: 43, Tissue: lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, follow-up: lost for follow-up
|
Nodular lymphocyte predominant Hodgkin's lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188671
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188671/suppl/GSM188671.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188672 | GPL570 |
|
NLPHL_lymph_node_case9
|
lymph node affected by NLPHL
|
Gender: male, Age: 25, Tissue: lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage: IA, follow-up: 11 years; status at last follow-up: alive without disease
|
Nodular lymphocyte predominant Hodgkin's lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188672
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188672/suppl/GSM188672.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188673 | GPL570 |
|
NLPHL_lymph_node_case10
|
lymph node affected by NLPHL
|
Gender: male, Age: 25, Tissue: lymph node taken at diagnosis affected by nodular lymphocyte predominant Hodgkin's lymphoma, An Arbor Stage: IA, follow-up: 12 years; status at last follow-up: alive without disease
|
Nodular lymphocyte predominant Hodgkin's lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188673
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188673/suppl/GSM188673.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188674 | GPL570 |
|
THRBL_lymph_node_case3
|
lymph node affected by THRBL
|
Gender: male, Age: 50, Tissue: lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage: IVA, IPI prognostic score: low intermediate, follow-up: 4 years; status at last follow-up: alive without disease
|
T cell/histiocyte rich B cell lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188674
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188674/suppl/GSM188674.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188675 | GPL570 |
|
THRBL_lymph_node_case4
|
lymph node affected by THRBL
|
Gender: male, Age: 52, Tissue: lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage: IV, IPI prognostic score: high, follow-up: 3 years; status at last follow-up: alive with disease
|
T cell/histiocyte rich B cell lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188675
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188675/suppl/GSM188675.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188676 | GPL570 |
|
THRBL_lymph_node_case5
|
lymph node affected by THRBL
|
Gender: male, Age: 62, Tissue: lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage: IIIA, IPI prognostic score: low intermediate, follow-up: 3 years; status at last follow-up: alive without disease
|
T cell/histiocyte rich B cell lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188676
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188676/suppl/GSM188676.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188677 | GPL570 |
|
THRBL_lymph_node_case6
|
lymph node affected by THRBL
|
Gender: female, Age: 75, Tissue: lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage: IIIA, IPI prognostic score: low intermediate, follow-up: <1 year; status at last follow-up: death with disease
|
T cell/histiocyte rich B cell lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188677
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188677/suppl/GSM188677.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188678 | GPL570 |
|
THRBL_lymph_node_case7
|
lymph node affected by THRBL
|
Gender: male, Age: 47, Tissue: lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage: IVB, IPI prognostic score: high intermediate, follow-up: <1 year; status at last follow-up: death with disease
|
T cell/histiocyte rich B cell lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188678
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188678/suppl/GSM188678.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188679 | GPL570 |
|
THRBL_lymph_node_case8
|
lymph node affected by THRBL
|
Gender: male, Age: 45, Tissue: lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage: IVB, IPI prognostic score: high, follow-up: 1 year; status at last follow-up: death with disease
|
T cell/histiocyte rich B cell lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188679
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188679/suppl/GSM188679.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188680 | GPL570 |
|
Normal_reactive_lymph_node_pool
|
Reference sample, pool of 5 lymph nodes with follicular hyperplasia
|
Tissue: lymph node with follicular hyperplasia, nr of pooled samples: 5
|
Reference sample, pool of 5 lymph nodes with follicular hyperplasia
|
| Sample_geo_accession | GSM188680
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188680/suppl/GSM188680.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188681 | GPL570 |
|
THRBL_spleen_case1
|
spleen affected by THRBL
|
Gender: male, Age: 40, Tissue: spleen taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage: IVB, IPI prognostic score: low intermediate, follow-up: 2 years; status at last follow-up: death with disease
|
T cell/histiocyte rich B cell lymphoma affecting a spleen
|
| Sample_geo_accession | GSM188681
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188681/suppl/GSM188681.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
|
GSM188682 | GPL570 |
|
THRBL_lymph_node_case9
|
lymph node affected by THRBL
|
Gender: male, Age: 45, Tissue: lymph node taken at diagnosis affected by T cell/histiocyte rich B cell lymphoma, An Arbor Stage: III, follow-up: <2 years; status at last follow-up: death with disease
|
T cell/histiocyte rich B cell lymphoma affecting a lymph node
|
| Sample_geo_accession | GSM188682
| | Sample_status | Public on Nov 27 2009
| | Sample_submission_date | May 14 2007
| | Sample_last_update_date | Nov 27 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_biomaterial_provider_ch1 | Department of pathology, University Hospitals Leuven
| | Sample_treatment_protocol_ch1 | tissue blocs were kept at -80° till use
| | Sample_growth_protocol_ch1 | Fresh frozen tissue blocs were kept at -80° till use. They were transported on dry ice to the cryostat where a number (depending on the size of the bloc) of 20 micron thick sections were cut and put into a labeled, 2.0 ml microcentrifuge tube. At the end an extra 3 micron thick section was taken for HE staining.
| | Sample_molecule_ch1 | cytoplasmic RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from 20 micron sections of each frozen tissue sample, using the TriZol reagent (Invitrogen, Merelbeke, Belgium) followed by purification using the RNaesy mini kit (Qiagen, Venlo, The Netherlands), according to the manufacturers recommendations. RNA quality, integrity and concentration were measured using a nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA.
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were normalized using GC-RMA. The package gcrma in Bioconductor was used for this (R version 2.3.1)
| | Sample_platform_id | GPL570
| | Sample_contact_name | Joke,,Allemeersch
| | Sample_contact_email | joke.allemeersch@vib.be
| | Sample_contact_phone | +32(0)16 37 31 26
| | Sample_contact_department | Nucleomics Core
| | Sample_contact_institute | Flanders Institute for Biotechnology (VIB)
| | Sample_contact_address | Herestraat 49 Box 816
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | B-3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM188nnn/GSM188682/suppl/GSM188682.CEL.gz
| | Sample_series_id | GSE7788
| | Sample_data_row_count | 54675
| | |
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